The basic genetic characteristics, important functional genes, and entire transcriptome of Solen grandis Dunker were investigated by constructing a full-length cDNA library with the ‘switching mechanism at the 5'...The basic genetic characteristics, important functional genes, and entire transcriptome of Solen grandis Dunker were investigated by constructing a full-length cDNA library with the ‘switching mechanism at the 5'-end of the RNA transcript'(SMART) technique. Total RNA was isolated from the immune-relevant tissues, gills and hemocytes, using the Trizol reagent, and cDNA fragments were digested with Sfi I before being ligated to the pBluescript II SK* vector. The cDNA library had a titer of 1048 cfu μL-1 and a storage capacity of 1.05×106 cfu. Approximately 98% of the clones in the library were recombinants, and the fragment lengths of insert cDNA ranged from 0.8 kb to 3.0 kb. A total of 2038 expressed sequence tags were successfully sequenced and clustered into 965 unigenes. BLASTN analysis showed that 240 sequences were highly similar to the known genes(E-value < 1e-5; percent identity >80%), accounting for 25% of the total unigenes. According to the Gene Ontology, these unigenes were related to several biological processes, including cell structure, signal transport, protein synthesis, transcription, energy metabolism, and immunity. Fifteen of the identified sequences were related to defense and immunity. The full-length cDNA sequence of HSC70 was obtained. The cDNA library of S. grandis provided a useful resource for future researches of functional genomics related to stress tolerance, immunity, and other physiological activities.展开更多
In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious...In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious.This study developed a novel,rapid,and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing(TEAseq).Using TEAseq,we systemically profiled the Dissociation(Ds)insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background.The Ac-containing individuals were excluded for getting rid of the potential somatic insertions.We characterized 35,696 germinal Ds insertions tagging 10,323 genes,representing approximately 23.3%of the total genes in the maize genome.The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci,and insertions occurred preferentially in gene body regions.Furthermore,we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development.We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations.Overall,our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.展开更多
<div style="text-align:justify;"> <span style="font-family:Verdana;">The rumen microbiome plays an essential role in ruminant physiology, nutrition and pathology as well as host immunit...<div style="text-align:justify;"> <span style="font-family:Verdana;">The rumen microbiome plays an essential role in ruminant physiology, nutrition and pathology as well as host immunity. A better understanding of rumen</span><span style="font-family:Verdana;"> microbial processes and identification of which populations are responsible for specific functions within the rumen microbiome will lead to better management and sustainable utilization of the available feed base while maintaining a low environmental impact. Recent advance in the culture independent method of microbiology such as metagenomics, unravels potentially the rumen microbial process. Th</span><span style="font-family:Verdana;">ere are two basic types of metagenomics studies: Sequence-based and function-based metagenomics. Sequence-based metagenomics involves sequencing and analysis of DNA from environmental samples. Its purpose is to assemble genomes, identify genes, find complete metabolic pathways, and compare organisms of different communities. Whereas functional metagenomics is the study of the collective genome of a microbial community by expressing it in a foreign host usually </span><i><span style="font-family:Verdana;">Escherichia</span></i> <i><span style="font-family:Verdana;">coli</span></i><span style="font-family:Verdana;"> (</span><i><span style="font-family:Verdana;">E.</span></i> <i><span style="font-family:Verdana;">coli</span></i><span style="font-family:Verdana;">)</span><i><span style="font-family:Verdana;">.</span></i><span style="font-family:Verdana;"> It is a promising approach unearthing novel enzymes even from yet to culture rumen microbiota. Further advances in the screening techniques promise vast opportunities to rumen microbiologists, and animal nutritionist. The identification of novel enzyme through functional metagenomics consists of three parts: rumen sample collection;DNA library construction and screening of individual clone. Functional metagenomics was successfully applied to identify different antibiotics, hydrolytic enzymes, antibiotic resistance genes, and many other functions;moreover, it allowed characterization of genes encoding enzymes with a particular activity, which represents completely novel sequence. There are a number of outputs from functionally screened rumen product such as carbohydrate active enzymes (CAZymes) that can break down plant cell walls. Company involved commercialization of metagenomics research such as Syngenta, Genencor International, BRAIN etc., has produced many biological molecules of commercial interest. The aim of this paper is to elucidate functional metagenomics, from rumen environment and its potential for commercial purpose.</span> </div>展开更多
Based on a questionnaire survey,the paper made a comparative study on the changes of traditional library positions within the context of the emerging professional positions and functional units at some large academic ...Based on a questionnaire survey,the paper made a comparative study on the changes of traditional library positions within the context of the emerging professional positions and functional units at some large academic libraries in China and in the United States from 1998 to 2007.It describes how some of the library professional positions and functional units have gone through a time period of intensified and proactive position allocation realignment in terms of their rise,decline,fission and/or fusion within the administrative context of their library's evolving changes in missions,objectives and service delivery structure under the impact of the rapid development of information technologies.Such changes are graphically demonstrated in several charts in this paper to highlight the evolutionary development of academic librarianship in general and the waves of changes for library position reallocations in specific in the ten-year period under study.It is believed that such a study can be useful for discerning the overall developing trend of academic librarianship,especially in the area of the rising professional and social status of academic librarianship during this period.The movement of library position allocation realignment was a corresponding response at the time to the influx of applicable information technologies to the library scene.It not only made the library operation to become'leaner and meaner,' but also gave added impetus to the rise of the professional and social status of their practitioners in the society due to the latter's enhanced service delivery innovations and capabilities for meeting their constituencies' timely information needs more satisfactorily.展开更多
基金supported by the Shandong Program of Agriculture Thoroughbred Project to Xiangquan Liu,the Marine Special Research Foundation of China for Non-profit Public Industry(No.200805031)Taishan Scholar position funding of Aquatic Animal Nutrition and Feed to Linmin Zhang and NSFC funding(No.31202025)
文摘The basic genetic characteristics, important functional genes, and entire transcriptome of Solen grandis Dunker were investigated by constructing a full-length cDNA library with the ‘switching mechanism at the 5'-end of the RNA transcript'(SMART) technique. Total RNA was isolated from the immune-relevant tissues, gills and hemocytes, using the Trizol reagent, and cDNA fragments were digested with Sfi I before being ligated to the pBluescript II SK* vector. The cDNA library had a titer of 1048 cfu μL-1 and a storage capacity of 1.05×106 cfu. Approximately 98% of the clones in the library were recombinants, and the fragment lengths of insert cDNA ranged from 0.8 kb to 3.0 kb. A total of 2038 expressed sequence tags were successfully sequenced and clustered into 965 unigenes. BLASTN analysis showed that 240 sequences were highly similar to the known genes(E-value < 1e-5; percent identity >80%), accounting for 25% of the total unigenes. According to the Gene Ontology, these unigenes were related to several biological processes, including cell structure, signal transport, protein synthesis, transcription, energy metabolism, and immunity. Fifteen of the identified sequences were related to defense and immunity. The full-length cDNA sequence of HSC70 was obtained. The cDNA library of S. grandis provided a useful resource for future researches of functional genomics related to stress tolerance, immunity, and other physiological activities.
基金the Ministry of Science and Technology of China(2016YFD0101000 and 2016YFD0101001)the Natural Science Foundation of China(31901595).
文摘In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious.This study developed a novel,rapid,and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing(TEAseq).Using TEAseq,we systemically profiled the Dissociation(Ds)insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background.The Ac-containing individuals were excluded for getting rid of the potential somatic insertions.We characterized 35,696 germinal Ds insertions tagging 10,323 genes,representing approximately 23.3%of the total genes in the maize genome.The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci,and insertions occurred preferentially in gene body regions.Furthermore,we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development.We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations.Overall,our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.
文摘<div style="text-align:justify;"> <span style="font-family:Verdana;">The rumen microbiome plays an essential role in ruminant physiology, nutrition and pathology as well as host immunity. A better understanding of rumen</span><span style="font-family:Verdana;"> microbial processes and identification of which populations are responsible for specific functions within the rumen microbiome will lead to better management and sustainable utilization of the available feed base while maintaining a low environmental impact. Recent advance in the culture independent method of microbiology such as metagenomics, unravels potentially the rumen microbial process. Th</span><span style="font-family:Verdana;">ere are two basic types of metagenomics studies: Sequence-based and function-based metagenomics. Sequence-based metagenomics involves sequencing and analysis of DNA from environmental samples. Its purpose is to assemble genomes, identify genes, find complete metabolic pathways, and compare organisms of different communities. Whereas functional metagenomics is the study of the collective genome of a microbial community by expressing it in a foreign host usually </span><i><span style="font-family:Verdana;">Escherichia</span></i> <i><span style="font-family:Verdana;">coli</span></i><span style="font-family:Verdana;"> (</span><i><span style="font-family:Verdana;">E.</span></i> <i><span style="font-family:Verdana;">coli</span></i><span style="font-family:Verdana;">)</span><i><span style="font-family:Verdana;">.</span></i><span style="font-family:Verdana;"> It is a promising approach unearthing novel enzymes even from yet to culture rumen microbiota. Further advances in the screening techniques promise vast opportunities to rumen microbiologists, and animal nutritionist. The identification of novel enzyme through functional metagenomics consists of three parts: rumen sample collection;DNA library construction and screening of individual clone. Functional metagenomics was successfully applied to identify different antibiotics, hydrolytic enzymes, antibiotic resistance genes, and many other functions;moreover, it allowed characterization of genes encoding enzymes with a particular activity, which represents completely novel sequence. There are a number of outputs from functionally screened rumen product such as carbohydrate active enzymes (CAZymes) that can break down plant cell walls. Company involved commercialization of metagenomics research such as Syngenta, Genencor International, BRAIN etc., has produced many biological molecules of commercial interest. The aim of this paper is to elucidate functional metagenomics, from rumen environment and its potential for commercial purpose.</span> </div>
文摘Based on a questionnaire survey,the paper made a comparative study on the changes of traditional library positions within the context of the emerging professional positions and functional units at some large academic libraries in China and in the United States from 1998 to 2007.It describes how some of the library professional positions and functional units have gone through a time period of intensified and proactive position allocation realignment in terms of their rise,decline,fission and/or fusion within the administrative context of their library's evolving changes in missions,objectives and service delivery structure under the impact of the rapid development of information technologies.Such changes are graphically demonstrated in several charts in this paper to highlight the evolutionary development of academic librarianship in general and the waves of changes for library position reallocations in specific in the ten-year period under study.It is believed that such a study can be useful for discerning the overall developing trend of academic librarianship,especially in the area of the rising professional and social status of academic librarianship during this period.The movement of library position allocation realignment was a corresponding response at the time to the influx of applicable information technologies to the library scene.It not only made the library operation to become'leaner and meaner,' but also gave added impetus to the rise of the professional and social status of their practitioners in the society due to the latter's enhanced service delivery innovations and capabilities for meeting their constituencies' timely information needs more satisfactorily.
